C++ compiling not going anywhere


Might be a Stan or brms issue. I am using a Mac Os. I can’t get past this step now with even with a trivial model with 100 data points:

Compiling the C++ model
Start sampling
starting worker pid=1995 on localhost:11438 at 16:19:18.515

It just continues to load but nothing happens and it doesn’t go past this step.

I am using the latest version of R studio, latest version of brms installed from Github, and uninstalled and reinstalled stan following all online instructions again.

This problem seems to be triggered when I run a more complex brms model and then I decide to stop it midway. This seems to work fine. Nothing stalls but then I’m unable to run other brms() tasks afterwards. Even after shutting down the cpu processes and restarting my computer it is not going away now. And uninstalling and reinstalling rstan and brms.

Here is results from file:///Users/Ilan/.R/Makevars:

CXXFLAGS=-O3 -Wno-unused-variable -Wno-unused-function -Wno-unused-local-typedefs

CXX=clang++ -arch x86_64 -ftemplate-depth-256

CXXFLAGS=-O3 -Wno-unused-variable -Wno-unused-function -Wno-unused-local-typedefs

CXX=clang++ -arch x86_64 -ftemplate-depth-256

CXXFLAGS=-O3 -Wno-unused-variable -Wno-unused-function -Wno-unused-local-typedefs #set_by_rstan

CXX=clang++ -arch x86_64 -ftemplate-depth-256
R_XTRA_CPPFLAGS = -I$(R_INCLUDE_DIR) #set_by_rstan
CXX14FLAGS=-O3 -march=native -mtune=native
CXX14FLAGS += -arch x86_64 -ftemplate-depth-256

And here is sessioninfo():

R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] bayesplot_1.6.0 sjPlot_2.6.2 brms_2.8.8 Rcpp_1.0.1 stargazer_5.2.2
[6] ggeffects_0.9.0 jtools_2.0.1 broom_0.5.2 magrittr_1.5 scales_1.0.0
[11] zoo_1.8-5 Hmisc_4.2-0 Formula_1.2-3 survival_2.44-1.1 lattice_0.20-38
[16] gridExtra_2.3 ggforce_0.2.2 xtable_1.8-4 modelr_0.1.4 ggthemes_4.1.1
[21] forcats_0.4.0 stringr_1.4.0 dplyr_0.8.0.1 purrr_0.3.2 readr_1.3.1
[26] tidyr_0.8.3 tibble_2.1.1 ggplot2_3.1.1 tidyverse_1.2.1

loaded via a namespace (and not attached):
[1] readxl_1.3.1 backports_1.1.4 plyr_1.8.4 igraph_1.2.4.1
[5] lazyeval_0.2.2 TMB_1.7.15 splines_3.5.1 crosstalk_1.0.0
[9] TH.data_1.0-10 rstantools_1.5.1 inline_0.3.15 digest_0.6.18
[13] htmltools_0.3.6 rsconnect_0.8.13 checkmate_1.9.1 cluster_2.0.8
[17] matrixStats_0.54.0 xts_0.11-2 sandwich_2.5-1 prettyunits_1.0.2
[21] colorspace_1.4-1 rvest_0.3.3 haven_2.1.0 xfun_0.6
[25] callr_3.2.0 crayon_1.3.4 jsonlite_1.6 lme4_1.1-21
[29] glue_1.3.1 polyclip_1.10-0 gtable_0.3.0 emmeans_1.3.4
[33] sjstats_0.17.4 sjmisc_2.7.9 pkgbuild_1.0.3 rstan_2.18.2
[37] abind_1.4-5 mvtnorm_1.0-10 miniUI_0.1.1.1 htmlTable_1.13.1
[41] foreign_0.8-71 stats4_3.5.1 StanHeaders_2.18.1 DT_0.5
[45] htmlwidgets_1.3 httr_1.4.0 threejs_0.3.1 RColorBrewer_1.1-2
[49] acepack_1.4.1 pkgconfig_2.0.2 loo_2.1.0 farver_1.1.0
[53] nnet_7.3-12 tidyselect_0.2.5 rlang_0.3.4 reshape2_1.4.3
[57] later_0.8.0 munsell_0.5.0 cellranger_1.1.0 tools_3.5.1
[61] cli_1.1.0 generics_0.0.2 sjlabelled_1.0.17 ggridges_0.5.1
[65] processx_3.3.0 knitr_1.22 pander_0.6.3 nlme_3.1-139
[69] mime_0.6 xml2_1.2.0 compiler_3.5.1 shinythemes_1.1.2
[73] rstudioapi_0.10 tweenr_1.0.1 stringi_1.4.3 ps_1.3.0
[77] Brobdingnag_1.2-6 Matrix_1.2-17 psych_1.8.12 nloptr_1.2.1
[81] markdown_0.9 shinyjs_1.0 pillar_1.3.1 bridgesampling_0.6-0
[85] estimability_1.3 data.table_1.12.2 insight_0.2.0 httpuv_1.5.1
[89] R6_2.4.0 latticeExtra_0.6-28 promises_1.0.1 codetools_0.2-16
[93] boot_1.3-20 colourpicker_1.0 MASS_7.3-51.4 gtools_3.8.1
[97] assertthat_0.2.1 withr_2.1.2 shinystan_2.5.0 mnormt_1.5-5
[101] multcomp_1.4-10 parallel_3.5.1 hms_0.4.2 grid_3.5.1
[105] rpart_4.1-15 coda_0.19-2 glmmTMB_0.2.3 minqa_1.2.4
[109] shiny_1.3.2 lubridate_1.7.4 base64enc_0.1-3 dygraphs_1.1.1.6

Many thanks! Sorry for the hassle.

I reinstalled pretty much everything: R and all tools, XQuartz, Xcode, etc. It is working now.

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